Not related to your problem but thought I'd mention that its possible to 'reset' the USB ports via the command line without replugging. I don't have it to hand but it's mentioned over on the Pi forums with some discussion and pictures of different cmds to reset different ports. Off the top of my head you can reset 2 ports at a time (top pair or bottom pair) or all 4 at once. Quite handy for remote management.
This let me a rabbit hole, but found a tool called devcon.exe that Microsoft puts out. In theory, you can restart USB controllers or USB devices. I had cgminer running and 2Pac would not restart (as it was being used). I've had better luck restarting 2Pac after I quit cgminer, restart the USB devices via devcon.exe (devcon.exe restart *PID_EA60*) , then restart cgminer. Put in a batch file loop. Your mileage may vary... Otherwise, I'm going back to USB HuB with hard power switch and a power timer that will turn off USB HUB every hour.